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The development of lung adenocarcinoma (LUAD) is intricately linked with cell cycle regulation and epithelial-mesenchymal transition (EMT). Our study, leveraging bioinformatics and database analysis, identified FUCA2 as a key gene influencing the prognosis and progression of LUAD. We observed that FUCA2 is highly expressed in LUAD and correlates with poor outcomes. Functionally, we assessed the role of this gene through cell cloning, scratch assays, transwell migration, and western blotting, revealing that FUCA2 knockdown significantly inhibits tumor cell proliferation and migration, downregulates the expression of cell cycle and EMT-related proteins, and markedly reduces tumor burden. Mechanistically, pathway enrichment analysis identified GGH as a downstream target of FUCA2. Knockdown of GGH similarly inhibits the proliferation, migration, and cell cycle progression of LUAD cells. FUCA2 upregulates GGH to modulate cell cycle and EMT in LUAD. Collectively, our findings indicate that the FUCA2/GGH axis promotes LUAD progression by regulating cell cycle and EMT., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

YBX1, a DNA-/RNA-binding protein, is implicated in various diseases, yet its role in intimal hyperplasia (IH) remains unclear. This study investigates YBX1's function in rat aortic smooth muscle cells (RASMCs) through knockdown experiments. Results show that YBX1 knockdown reduces cell proliferation and migration while inducing apoptosis. ELISA and western blot analyses revealed increased levels of the anti-inflammatory factor IL10 and markers for phenotypic transformation, Calponin and Myocardin. Transcriptome sequencing identified 1598 differentially expressed genes (DEGs), with 347 upregulated and 1251 downregulated. Upregulated DEGs were linked to pathways like ECM-receptor interaction and Wnt signalling, while downregulated genes involved cell cycle and p53 signalling. Additionally, 629 significant alternative splicing events were noted, primarily affecting pathways related to cell division and migration. Integrated analysis of YBX1-bound RNAs and RNA-seq data highlighted key DEGs, such as CCNB1 and TPM1, which are crucial for vascular cell behaviour. This study underscores YBX1's vital role in RASMCs and suggests potential therapeutic targets for IH treatment., (© 2025 The Author(s). Journal of Cellular and Molecular Medicine published by Foundation for Cellular and Molecular Medicine and John Wiley & Sons Ltd.)

Background: In B-cell precursor acute lymphoblastic leukemia (BCP-ALL), chromosomal translocations are strongly associated with prognoses. RNA sequencing (RNA-seq) is a powerful technology that reveals a close correlation between types of translocation and patterns of gene expression in clinical samples of BCP-ALL. Cancer cell lines are powerful research tools, and thus, we built a larger series of BCP-ALL cell lines and performed RNA-seq analysis to confirm their utility as a model system., Methods: We performed RNA-seq in a total of 94 BCP-ALL cell lines, including 80 cell lines with 8 representative types of translocations., Results: In the UMAP visualization, a close association was confirmed between the types of fusion genes and patterns of gene expression. In the cluster analysis of the gene expression profile, each type of fusion gene showed a clear association with the expression profile in the top 51 variable genes. Of clinical importance, the majority of the top variable genes in the BCP-ALL cell lines also showed a significant association with the types of fusion genes in the clinical samples. When an association of 125 cell cycle-related genes with the percentage of S and G2/M phases in 67 cell lines was evaluated, a significant positive correlation with cell cycle progression was confirmed in 10 cell cycle-related genes (HDAC2, CDC23, YWHAG, MAD2L1, CCNH, ANAPC7, CDC6, ANAPC5, ORC3, andRBX1). Moreover, significant upregulation and downregulation of 40 and 10 genes, respectively, were observed in the cell lines established at relapse compared with those established at diagnosis. Four (SP6, CCNE1, HIST1H2BH, and DECR2) and two (EVI2B and SYN1) of these genes were also significantly higher and lower, respectively, in the clinical samples at relapse than in those at diagnosis., Conclusion: Large series of BCP-ALL cell lines is a powerful research tool for studying the mechanisms of leukemogenesis and the disease progression of BCP-ALL., (© 2025 The Author(s). Cancer Medicine published by John Wiley & Sons Ltd.)

Objective: This study aims to identify miRNA-mediated regulation of the cell cycle in oral tongue cancer., Design: Comprehensive computational analysis was performed on the GEO dataset "GSE168227". DIANA Tool-mir path v.3, STRING, Cytoscape 3.6.0, Enrichr, and TargetScan Human 7.2 were utilized to identify and analyze miRNAs and their targets in oral tongue cancer. The identified miRNA and its target genes were further analyzed in oral tongue cancer patients using qPCR and immunohistochemistry (IHC)., Results: Computational analysis revealed miR-17 as a differentially expressed miRNA in oral tongue cancer. Database analysis indicated potential binding sites of miR-17 for CDKN1A and CCND1 mRNA at 3'-UTR. In oral tongue cancer samples, miR-17, CDKN1A, and CCND1expression were upregulated compared to controls. IHC demonstrated overexpression of p21 and Cyclin D1 across various tumor grades, with predominant cytoplasmic expression of p21 observed in oral tongue cancer samples., Conclusion: The findings suggest that miR-17 may regulate the G1-S transition of the cell cycle in oral tongue cancer. Further validation and functional studies are warranted to confirm their role as biomarkers., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2025 Elsevier Ltd. All rights reserved.)

The faithful production of primordial germ cells (PGCs) in vitro opens a wide range of novel applications in reproductive biology and medicine. However, the reproducibility of PGCs culture conditions across different laboratories or breeds remains a challenge. Therefore, it is necessary to research the molecular dynamics that lead to the gradual establishment of cultured PGCs lines network. Here, the results of single-cell RNA-seq indicated that the cell cycle drove cellular heterogeneity. The active populations engaged in PGC self-renewal and the characteristics of the aging cell fate have been identified. The active self-renewal populations presented a rising expression of DNA repair genes, couple with a high proportion of cells in G1/S phase and a low frequency of cells in G2 phase. Notably, Hippo, FoxO, AMPK and MAPK pathways are active within these populations. The combination of six activator or inhibitors, targeting these active pathways, resulted in a significantly higher proliferation rate of PGCs and an increased number of cells entering the G1 and S phases. Importantly, they greatly reduced the establishment time to a minimum of 26 days and increased the efficiency of male PGC line establishment to 59 % in FS medium. Our results provided several new insights into the PGCs., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

During X chromosome inactivation (XCI), Xist RNA establishes silencing by coating the chromosome in cis and binding diverse proteins to promote formation of a heterochromatic domain. However, Xist repeat B role beyond initiation of XCI remains unclear. Here, we find that loss of Xist repeat B in female mice allows survival and leads to a small body size persisting throughout life. Epigenetic and transcriptomic analyses reveal low levels of H3K27me3 and H2AK119ub occupancy on the X chromosome, except in certain CpG island regions, and partial reactivation of X-linked genes on the inactive X across multiple tissues. Notably, overdosage of Usp9x promotes centrosome amplification and chromosome instability. We further demonstrate that Usp9x overdosage alters asymmetric cell division, thereby affecting the process of cell differentiation. Thus, Xist repeat B is necessary for gene-specific silencing during XCI maintenance and impacts cell proliferation and differentiation during development. This provides insights into repeat B importance in maintaining XCI., (© The Author(s) 2025. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Manipulating spawning seasons of Atlantic salmon (Salmo salar) is a common practice to facilitate year-round harvesting in salmon aquaculture. This process involves adjusting water temperature and light regime to control female broodstock maturation. However, recent studies have indicated that altered spawning seasons can significantly affect the nutritional status and growth performance of the offspring. Therefore, gaining a deeper understanding of the biological regulations influenced by these alterations is crucial to enhance the growth performance of fish over multiple generations. In this study, we investigated omics data from four different spawning seasons achieved through recirculating aquaculture systems (RAS) and sea-pen-based approaches. In addition to the normal spawning season in November (sea-pen), three altered seasons were designated: off-season (five-month advance, RAS), early season (two-month advance, sea-pen), and late season (two-month delay, sea-pen). We conducted comprehensive gene expression and DNA methylation analysis on liver samples collected from the start-feeding larvae of the next generation. Our results revealed distinct gene expression and DNA methylation patterns associated with the altered spawning seasons. Specifically, offspring from RAS-based off-season exhibited altered lipid-mediated regulation, while those from sea-pen-based early and late seasons showed changes in cellular processes, particularly in cell cycle regulation when compared to the normal season. The consequences of our findings are significant for growth and health, potentially providing information for developing valuable tools for assessing growth potential and optimizing production strategies in aquaculture., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2025 Saito et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Protein phosphatase PPM1B, a member of the serine/threonine phosphatase family, has been implicated in various human cancers. In this study, our objective was to investigate the role of PPM1B in GC growth and explore the underlying mechanisms. Our findings revealed that PPM1B expression was downregulated in GC tissues, and higher levels of PPM1B expression were associated with improved overall survival in GC patients. Overexpression of PPM1B significantly inhibited cell proliferation, induced G1 phase cell cycle arrest, and suppressed tumor growth. Conversely, knockdown or knockout of PPM1B yielded opposite effects. Mechanistically, we identified that PPM1B exerted its inhibitory role in GC cell growth and cell cycle regulation through the TRIM25/PPM1B/CDK2 signaling pathway. Specifically, we demonstrated that TRIM25 physically interacts with PPM1B, leading to enhanced degradation of PPM1B and subsequent modulation of CDK2 phosphorylation and GC cell growth. PPM1B emerges as a potential prognostic biomarker and therapeutic target in GC. These findings hold clinical significance by offering opportunities to improve diagnosis and treatment strategies for GC patients. Furthermore, this study provides novel insights into the pathogenesis and progression of GC, expanding our understanding of this disease., Competing Interests: Declarations. Competing interests: The authors declare no competing interests. Ethical approval: All animal studies were approved by the Fujian Medical University’s laboratory animal ethics committee and Chinese government guidelines for animal experiments. All methods used in animal experiments were carried out in accordance with relevant guidelines, and handled according to standard use protocols and animal welfare regulations, and we also confirmed that all animal methods were reported in accordance with ARRIVE guidelines ( http://arriveguidelines.org ) for the reporting of animal experiments., (© 2025. The Author(s).)

Breast cancer is a highly heterogeneous disease; hence, it is crucial to understand its biology and identify new targets for the development of effective treatments. Galectin-1 is known to play an oncogenic role in breast cancer progression. It is known that oncogenic factors can influence cancer progression through interactions with miRNAs. The purpose of this study is to identify the clinical significance and biological role of galectin-1 and miR-22-3p in cancer progression according to the molecular subtype of breast cancer. We analyzed the expression of galectin-1 and miR-22-3p using cancer tissues and the correlation with clinical pathological characteristics. In addition, we investigated the regulation of the cell cycle and EMT processes of cancer progression through the galectin-1/miR-22-3p axis using cell lines of different breast cancer subtypes. miR-22-3p negatively regulates galectin-1 expression and the two molecules have opposite patterns of oncogenic and tumor-suppressive functions, respectively; furthermore, these two molecules are associated with metastasis-free survival. Cell experiments showed that miR-22-3p overexpression and galectin-1 knockdown inhibited the proliferation and invasion of breast cancer cells. Galectin-1 regulates different cancer progression pathways depending on the molecular subtype. In hormone receptor-positive breast cancer cells, galectin-1 knockdown mainly inhibited cell cycle-related substances and induced G0/G1 arrest, whereas in triple-negative breast cancer cells, it suppressed molecules related to the epithelial-mesenchymal transition pathway. In conclusion, the miR-22-3p/galectin-1 axis regulates different cancer metastasis mechanisms depending on the specific molecular subtype of breast cancer, and miR-22-3p/galectin-1 axis modulation may be a novel target for molecular subtype-specific personalized treatment.

Clb1 and Clb2 are functionally redundant B-type cyclins, and the clb1Δ clb2Δ double mutant is lethal. In normal mitotic growth, Clb2 plays the central role in the G2-M progression. We previously demonstrated that the RNA-binding protein Puf5 positively regulates CLB1 expression by downregulating expression of the repressor Ixr1. The decreased expression of CLB1 by the puf5Δ mutation caused a severe growth defect of the puf5Δ clb2Δ double mutant. On the contrary, CLB2 expression was unchanged between wild-type strain and puf5Δ mutant in unsynchronized cultures, and the puf5Δ clb1Δ double mutant did not show growth retardation. Therefore, we assumed that CLB1 is the main target of Puf5 in the previous study. However, considering that CLB1 and CLB2 reportedly undergo a similar expression pattern during the cell cycle, we re-examined CLB2 expression in the puf5Δ mutant in cell cycle-synchronized cultures and found that CLB2 expression was decreased in the puf5Δ mutant strain. Deletion of IXR1 restored the decreased expression of CLB2 caused by the puf5Δ mutation. Moreover, we clarified that the decreased expression of CLB2 caused by the puf5Δ mutation resulted in the growth defect in the S-phase cyclin deficient condition: the puf5Δ clb1Δ clb5Δ clb6Δ quadruple mutant grew worse than clb1Δ clb5Δ clb6Δ triple mutant, and the slow growth of the puf5Δ clb1Δ clb5Δ clb6Δ quadruple mutant was suppressed by CLB2 overexpression. Moreover, the ixr1Δ mutation is known to be synthetically lethal with deletion of the DUN1 gene encoding the checkpoint kinase. We found that the clb2Δ mutation restored the lethality of ixr1Δ dun1Δ double mutant. Our results suggest that Puf5 and Ixr1 regulate the cell cycle-specific expression of both CLB1 and CLB2, that Clb5 and Clb6 have overlapping roles with Clb1 and Clb2, and that the regulation of CLB1 and CLB2 expression by Puf5 and Ixr1 is related to the function of Dun1 kinase., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2025 Sato et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Cyclin-dependent kinases (CDKs) are key regulators of cell cycle progression, in conjunction with cyclins. The cyclin-CDK system is highly conserved among eukaryotes, and CDK1 is considered essential for progression through the M phase. However, the extent to which cell cycle progression depends on CDK1 varies between cell types. Therefore, a range of cell types must be analyzed to comprehensively elucidate the role of CDK1. Cdk1-knockout mice exhibit lethality at an early developmental stage, specifically before the differentiation of various cell types. The aim of the present study was to characterize the effects of CDK1 deficiency in amphibian newts. Cdk1 was disrupted by injecting fertilized newt eggs with CRISPR/Cas9, and the resulting effects on embryonic development and cell proliferation were then evaluated. In both wild-type and Cdk1-crispant newt embryos, CDK1 protein was either stored in the egg until late embryogenesis or potentially derived from maternal mRNA, which may also be stored during this period. The embryos survived to the hatching stage, during which the cells responsible for forming the basic organs differentiated. To further characterize the long-term effects of Cdk1 knockout, parabiosis experiments were conducted using wild-type embryos and Cdk1 crispants. The results suggested that an endocycle occurred in the crispant larvae, as evidenced by increases in the size of several types of cells. It is anticipated that studies using newts will provide further insights into the role of Cdk1 in regulating the cell cycle., (© 2025 Japanese Society of Developmental Biologists.)

Long noncoding RNAs (lncRNAs) are involved in the host antiviral response, but how host lncRNAs interact with viral proteins remains unclear. The NS1 protein of avian influenza viruses can affect the interferon-dependent expression of several host lncRNAs, but the exact mechanism is unknown. To further investigate the molecular mechanism and functions of NS1 proteins and host lncRNAs, we performed RNA-immunoprecipitation sequencing assays on A549 cells transfected with the H5N1-NS1 gene. We identified multiple sets of host lncRNAs that interact with NS1. The results of the RNA pulldown assay indicated that PIK3CD-AS2 can directly interact with NS1 in vitro. Immunofluorescence confocal microscopy showed that these proteins were colocalized in the nucleus. Further studies revealed that PIK3CD-AS2 can also inhibit the transcription of NS1, which in turn affects the translation of the NS1 protein. PIK3CD-AS2 overexpression regulates NS1 protein-induced cell cycle arrest and initiates apoptosis. We hope this work will help elucidate the molecular mechanisms associated with NS1 proteins in the study of viral infections to promote the development of potential treatments for patients infected with avian influenza A viruses., Competing Interests: Declarations. Conflict of interest: The authors have no relevant financial or nonfinancial interests to disclose. Ethical approval: Not applicable., (© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Synthetic lethality exploits the genetic vulnerabilities of cancer cells to enable a targeted, precision approach to treat cancer 1 . Over the past 15 years, synthetic lethal cancer target discovery approaches have led to clinical successes of PARP inhibitors 2 and ushered several next-generation therapeutic targets such as WRN 3 , USP1 4 , PKMYT1 5 , POLQ 6 and PRMT5 7 into the clinic. Here we identify, in human cancer, a novel synthetic lethal interaction between the PELO-HBS1L and SKI complexes of the mRNA quality control pathway. In distinct genetic contexts, including 9p21.3-deleted and high microsatellite instability (MSI-H) tumours, we found that phenotypically destabilized SKI complex leads to dependence on the PELO-HBS1L ribosomal rescue complex. PELO-HBS1L and SKI complex synthetic lethality alters the normal cell cycle and drives the unfolded protein response through the activation of IRE1, as well as robust tumour growth inhibition. Our results indicate that PELO and HBS1L represent novel therapeutic targets whose dependence converges upon SKI complex destabilization, a common phenotypic biomarker in diverse genetic contexts representing a significant population of patients with cancer., Competing Interests: Competing interests: V.P., A.E.R., K.S., S.K., K.K., D.C., D.W., P.L., S.P., M.T., A.C., S.W., M.B.P., D.M., V.M., X.S., C.L., S.S., Z.D., G.B., D.V., B.B., J.A.M., W.N.P. and J.P.P. are employees of AbbVie., (© 2025. The Author(s).)

DNA is subject to continual damage, leaving each cell with thousands of individual DNA lesions at any given moment 1-3 . The efficiency of DNA repair means that most known classes of lesion have a half-life of minutes to hours 3,4 , but the extent to which DNA damage can persist for longer durations remains unknown. Here, using high-resolution phylogenetic trees from 89 donors, we identified mutations arising from 818 DNA lesions that persisted across multiple cell cycles in normal human stem cells from blood, liver and bronchial epithelium 5-12 . Persistent DNA lesions occurred at increased rates, with distinctive mutational signatures, in donors exposed to tobacco or chemotherapy, suggesting that they can arise from exogenous mutagens. In haematopoietic stem cells, persistent DNA lesions, probably from endogenous sources, generated the characteristic mutational signature SBS19 13 ; occurred steadily throughout life, including in utero; and endured for 2.2 years on average, with 15-25% of lesions lasting at least 3 years. We estimate that on average, a haematopoietic stem cell has approximately eight such lesions at any moment in time, half of which will generate a mutation with each cell cycle. Overall, 16% of mutations in blood cells are attributable to SBS19, and similar proportions of driver mutations in blood cancers exhibit this signature. These data indicate the existence of a family of DNA lesions that arise from endogenous and exogenous mutagens, are present in low numbers per genome, persist for months to years, and can generate a substantial fraction of the mutation burden of somatic cells., Competing Interests: Competing interests: P.J.C., M.R.S. and I.M. are co-founders, stock holders and consultants for Quotient Therapeutics Ltd. M.H. is a consultant for Quotient Therapeutics Ltd, AstraZeneca and Boston Scientific and has received unrestricted scientific grants from Pfizer. M.A.F. is a current employee and stockholder of AstraZeneca. A.M.R. is a senior editor at Nature Medicine, a Nature Portfolio journal. A.M.R. was not involved in the editorial handling of this Nature paper (journals within the Nature Portfolio are editorially independent). All other authors declare no competing interests., (© 2025. The Author(s).)

Long noncoding RNAs (lncRNAs) play pivotal roles in the development of human malignancies, though their involvement in oral squamous cell carcinoma (OSCC) remains incompletely understood. Using The Cancer Genome Atlas (TCGA) dataset, we analyzed expression of 7840 lncRNAs in primary head and neck squamous cell carcinoma (HNSCC) and found that upregulation of LINC02154 is associated with a poorer prognosis. LINC02154 knockdown in OSCC cell lines induced cell cycle arrest and apoptosis, and significantly attenuated tumor growth in vitro and in vivo. Notably, depletion of LINC02154 downregulated FOXM1, a master regulator of cell cycle-related genes. RNA pulldown and mass spectrometry analyses identified a series of proteins that could potentially interact with LINC02154, including HNRNPK and LRPPRC. HNRNPK stabilizes FOXM1 expression by interacting with the 3'-UTR of FOXM1 mRNA, which suggests LINC02154 and HNRNPK promote cell cycling by regulating FOXM1 expression. Additionally, LINC02154 positively regulates HNRNPK expression by inhibiting microRNAs targeting HNRPNK. Moreover, LINC02154 affects mitochondrial function by interacting with LRPPRC. Depletion of LINC02154 suppressed expression of mitochondrial genes, including MTCO1 and MTCO2, and inhibited mitochondrial respiratory function in OSCC cells. These results suggest that LINC02154 exerts its oncogenic effects by modulating the cell cycle and oxidative phosphorylation in OSCC, highlighting LINC02154 as a potential therapeutic target., (© 2024 The Author(s). Cancer Science published by John Wiley & Sons Australia, Ltd on behalf of Japanese Cancer Association.)

Introduction: Bladder cancer is a malignant neoplasm with increasing incidence rates. LncRNAs play an important role in cancer, including development, prognosis, and response to therapies. It is known that lncRNA SBF2-AS1 was associated with cell proliferation and worse prognosis in various tumor types, but its role remains incompletely understood in bladder cancer. In this context, our objective was to evaluate the effect of lncRNA SBF2-AS1 silencing on bladder cancer cells., Methods: J82 and UM-UC-3 high-grade bladder tumor cells were treated with two siRNAs specific for SBF2-AS1 to evaluate cytotoxicity, clonogenic survival, morphology, cell migration, and cell cycle progression., Results: Expression inhibition of SBF2-AS1 resulted in cytotoxicity, morphological changes, and decreased clone formation and cell migration. Cell cycle alterations were not observed., Conclusion: Our study revealed that SBF2-AS1 plays an oncogenic role and holds promise as a potential target for the treatment of bladder cancer., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

The prevalence of Alzheimer's disease (AD) is increasing as society ages. The details of AD pathogenesis have not been fully elucidated, and a comprehensive gene expression analysis of the process leading up to the onset of AD would be helpful for understanding the mechanism. We performed an RNA sequencing analysis on a cohort of 1227 Japanese blood samples, representing 424 AD patients, 543 individuals with mild cognitive impairment (MCI), and 260 cognitively normal (CN) individuals. A total of 883 and 1169 statistically significant differentially expressed genes (DEGs) were identified between CN and MCI (CN-MCI) and between MCI and AD (MCI-AD), respectively. Pathway analyses using these DEGs, followed by protein-protein interaction network analysis, revealed key roles of ribosomal function in MCI progression, whereas immune responses, cell cycle, and protein processing in endoplasmic reticulum were involved in AD progression. Our findings indicate that the onset of AD might be associated with gene expression changes in the immune system, cell cycle, and protein processing following alterations in the expression of ribosomal protein genes during the MCI stage, although validation using brain tissue samples will be necessary in the future. Given the known effectiveness of delaying MCI progression in preventing AD, the genes related to ribosomal function might emerge as biomarkers for early diagnosis., Competing Interests: Declarations. Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Rhabdomyosarcoma (RMS), the most common pediatric soft tissue sarcoma, arises in skeletal muscle and remains in an undifferentiated state due to transcriptional and post-transcriptional regulators. Among its subtypes, fusion-negative RMS (FN-RMS) accounts for the majority of diagnoses in the pediatric population. MicroRNAs (miRNAs) are non-coding RNAs that modulate cell identity via post-transcriptional regulation of messenger RNAs (mRNAs). In this study, we identify miRNAs impacting FN-RMS cell identity, revealing miR-449a and miR-340 as major regulators of the cell cycle and p53 signaling. Through miR-eCLIP technology, we demonstrate that miR-449a and miR-340 directly target transcripts involved in glycolysis and mitochondrial pyruvate transport, inhibiting the mitochondrial pyruvate carrier (MPC) complex. Pharmacological MPC inhibition induces a similar metabolic shift, reducing metastatic potential and leading to cell cycle exit. Overall, miR-449 and miR-340 orchestrate FN-RMS cell identity, positioning MPC inhibition as a strategy to shift FN-RMS cells toward a non-tumorigenic, quiescent state., Competing Interests: Declaration of interests S.-M.F. has received funding from Bayer AG, Merck, Black Belt Therapeutics, Gilead, and Alesta Therapeutics; has consulted for Fund+; and is on the advisory board of Alesta Therapeutics. E.P. and M.S. hold a patent on the use of miRs for the treatment or prevention of rhabdomyosarcoma., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Multiciliated cells (MCCs) ensure fluid circulation in various organs. Their differentiation is marked by the amplification of cilia-nucleating centrioles, driven by a genuine cell-cycle variant, which is characterized by wave-like expression of canonical and non-canonical cyclins such as Cyclin O (CCNO). Patients with CCNO mutations exhibit a subtype of primary ciliary dyskinesia called reduced generation of motile cilia (RGMC). Here, we show that Ccno is activated at the crossroads of the onset of MCC differentiation, the entry into the MCC cell-cycle variant, and the activation of the centriole biogenesis program. Its absence blocks the G 1 /S-like transition of the cell-cycle variant, interrupts the centriologenesis transcription program, and compromises the production of centrioles and cilia in mouse brain and human respiratory MCCs. Altogether, our study identifies CCNO as a core regulator of entry into the MCC cell-cycle variant and the interruption of this variant as one etiology of RGMC., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Genetic alterations play a pivotal role in leukemic clonal transformation, significantly influencing disease pathogenesis and clinical outcomes. Here, we report a novel fusion gene and investigate its pathogenic role in acute lymphoblastic leukemia (ALL). We engineer a transposon transfection system expressing the TOP2B::AFF2 transcript and introduce it into Ba/F3 cells. Functional studies, including proliferation, cell cycle, and apoptosis assays, were conducted to assess the fusion gene's impact. In vitro assays reveal that the TOP2B::AFF2 fusion significantly enhances Ba/F3 cell proliferation and G1/S phase transition while suppressing differentiation and apoptosis. This study identifies TOP2B::AFF2 as a potential oncogenic driver. However, further validation through in vivo studies are warranted to fully elucidate the fusion gene's role in leukemogenesis., Competing Interests: Declarations. Competing interests: The authors declare no competing interests. Ethics approval and consent to participate: The study was reviewed and approved by the Medical Ethics Committee of the Children’s Hospital of Chongqing Medical University with the approval file number 2024.138. All methods were performed in accordance with the Declaration of Helsinki. Consent statement: Written informed consent was obtained from the patient’s legal guardians (parents) prior to the investigation for the publication of any potentially identifiable images or data included in this article., (© 2025. The Author(s).)

Single-cell RNA-seq methods can be used to delineate cell types and states at unprecedented resolution but do little to explain why certain genes are expressed. Single-cell ATAC-seq and multiome (ATAC + RNA) have emerged to give a complementary view of the cell state. It is however unclear what additional information can be extracted from ATAC-seq data besides transcription factor binding sites. Here, we show that ATAC-seq telomere-like reads counter-inituively cannot be used to infer telomere length, as they mostly originate from the subtelomere, but can be used as a biomarker for chromatin condensation. Using long-read sequencing, we further show that modern hyperactive Tn5 does not duplicate 9 bp of its target sequence, contrary to common belief. We provide a new tool, Telomemore, which can quantify nonaligning subtelomeric reads. By analyzing several public datasets and generating new multiome fibroblast and B-cell atlases, we show how this new readout can aid single-cell data interpretation. We show how drivers of condensation processes can be inferred, and how it complements common RNA-seq-based cell cycle inference, which fails for monocytes. Telomemore-based analysis of the condensation state is thus a valuable complement to the single-cell analysis toolbox., (© The Author(s) 2025. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Centromeres are marked by the centromere-specific histone H3 variant CENP-A/CENH3. Throughout the cell cycle, the constitutive centromere-associated network is bound to CENP-A chromatin, but how this protein network modifies CENP-A nucleosome conformations in vivo is unknown. Here, we purify endogenous centromeric chromatin associated with the CENP-C complex across the cell cycle and analyze the structures by single-molecule imaging and biochemical assays. CENP-C complex-bound chromatin was refractory to MNase digestion. The CENP-C complex increased in height throughout the cell cycle culminating in mitosis, and the smaller CENP-C complex corresponds to the dimensions of in vitro reconstituted constitutive centromere-associated network. In addition, we found two distinct CENP-A nucleosomal configurations; the taller variant was associated with the CENP-C complex. Finally, CENP-A mutants partially corrected CENP-C overexpression-induced centromeric transcription and mitotic defects. In all, our data support a working model in which CENP-C is critical in regulating centromere homeostasis by supporting a unique higher order structure of centromeric chromatin and altering the accessibility of the centromeric chromatin fiber for transcriptional machinery., (© 2025 Melters et al.)

In this study, we investigated the role of lncRNA-NEF in modulating hepatic stellate cell (HSC) activation, a key process in liver fibrosis. Using the GSE78160 dataset, we identified lncRNA-NEF as downregulated in liver cirrhosis patients. Gene Ontology and KEGG analyses implicated it in transcriptional regulation and cell cycle control. We established an activated HSC model with TGF-β1-treated LX-2 cells and employed RT-qPCR and Western blot to assess lncRNA-NEF and ERK1/2 expression. Lentiviral transfection was used to overexpress lncRNA-NEF in activated LX-2 cells, and its effects on proliferation, apoptosis, and cell cycle were evaluated using EdU staining, CCK-8, Annexin-V PE/7-AAD, TUNEL, and PI-FACS analysis. Overexpression of lncRNA-NEF led to reduced cell proliferation, increased apoptosis, and cell cycle arrest at the S and G2/M phases. We also observed a decrease in ERK1/2, c-Fos, Collagen I, α-SMA, and Bcl-2 expression, and an increase in Caspase-3 expression, as confirmed by Western blot. These results suggest that lncRNA-NEF regulates HSC activation via the ERK1/2/c-Fos axis, potentially offering a therapeutic target for antifibrotic drug development. Our findings provide a molecular basis for understanding the role of lncRNAs in liver fibrosis and highlight the potential of lncRNA-NEF as a novel antifibrotic target., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests:Yu Xiaohui reports financial support was provided by Clinical Medical Research Center of Non-infectious Liver Disease of Gansu Province. Yu Xiaohui reports a relationship with Clinical Medical Research Center of Non-infectious Liver Disease of Gansu Province that includes: funding grants. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Background: Modulation of protein synthesis according to the physiological cues is maintained through tight control of Eukaryotic Elongation Factor 2 (eEF2), whose unique translocase activity is essential for cell viability. Phosphorylation of eEF2 at its Thr56 residue inactivates this function in translation. In our previous study we reported a novel mode of post-translational modification that promotes higher efficiency in T56 phosphorylation. Cyclin A/CDK2-mediated phosphorylation of eEF2 at the S595 residue is required for more potent phosphorylation at the Thr56, suggesting CDK2 takes a role in robust suppression of protein synthesis., Methods and Results: In the current study, we analyzed the cell cycle, proliferation, cell death, migration, colony formation, autophagy, and response to Cisplatin properties of the point-mutant variant of HCT116 cells that express the CDK2 mutant (S595A-eEF2) of eEF2. The knocked in S595A mutation resulted in decreased levels of T56 phosphorylation of eEF2, which appears to have similar biological consequences to other experimental manipulations such as silencing the activity of the kinase for the Thr56 residue, eEF2 Kinase (eEF2K)., Conclusion: Our findings indicate that interfering with the inhibition of eEF2 results in elevated protein synthesis in HCT116 cells and is associated with the progression of malignancy in the colorectal cancer cell line, where eEF2K activity could provide a tumor suppressive role., Competing Interests: Declarations. Ethical approval: N/A. The study does not involve any human or animal subjects. Competing interests: The authors declare no competing interests., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

Cyclin Dependent Kinases (CDKs) are closely connected to the regulation of cell cycle progression, having been first identified as the kinases able to drive cell division. In reality, the human genome contains 20 different CDKs, which can be divided in at least three different sub-family with different functions, mechanisms of regulation, expression patterns and subcellular localization. Most of these kinases play fundamental roles the normal physiology of eucaryotic cells; therefore, their deregulation is associated with the onset and/or progression of multiple human disease including but not limited to neoplastic and neurodegenerative conditions. Here, we describe the functions of CDKs, categorized into the three main functional groups in which they are classified, highlighting the most relevant pathways that drive their expression and functions. We then discuss the potential roles and deregulation of CDKs in human pathologies, with a particular focus on cancer, the human disease in which CDKs have been most extensively studied and explored as therapeutic targets. Finally, we discuss how CDKs inhibitors have become standard therapies in selected human cancers and propose novel ways of investigation to export their targeting from cancer to other relevant chronic diseases. We hope that the effort we made in collecting all available information on both the prominent and lesser-known CDK family members will help in identify and develop novel areas of research to improve the lives of patients affected by debilitating chronic diseases., Competing Interests: Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Background: Granulosa cell proliferation and survival are essential for normal ovarian function and follicular development. Long non-coding RNAs (lncRNAs) have emerged as important regulators of cell proliferation and differentiation. Nuclear paraspeckle assembly transcript 1 (NEAT1) has been implicated in various cellular processes, but its role in granulosa cell function remains unclear., Methods: We investigated the function of lncRNA NEAT1 in human ovarian granulosa-like tumor cells (KGN). The effects of NEAT1 overexpression or silencing on cell proliferation and cell cycle were evaluated using CCK-8 assays and flow cytometry. The interaction between NEAT1, miR-29a-3p, and IGF1 was examined using dual-luciferase reporter assays, qRT-PCR, and Western blot analysis., Results: NEAT1 promoted granulosa cell proliferation and cell cycle progression by indirectly upregulated IGF1 expression through acting as a molecular sponge for miR-29a-3p. Cell proliferation and G2/M phase proportions were increased by overexpression of NEAT1, whereas cell proliferation and G2/M phase proportions decreased with NEAT1 silencing. The effects of NEAT1 on cell proliferation and cell cycle-related proteins (CCNB1 and CDK2) were partially reversed by miR-29a-3p mimic, while miR-29a-3p inhibitor rescued the effects of NEAT1 silencing., Conclusion: LncRNA NEAT1 could promote ovarian granulosa cell proliferation and cell cycle progression via the miR-29a-3p/IGF1 axis in polycystic ovary syndrome. Further investigation of this mechanism in clinical samples may have implications for understanding ovarian physiology and pathology., Competing Interests: Declarations. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

The replication of the two chromosomes in the pathogenic bacterium Vibrio cholerae is coordinated by the binding of initiator protein RctB to a checkpoint sequence, crtS. Replication of crtS on the primary chromosome (Chr1) triggers replication of the secondary chromosome (Chr2), but the details are poorly understood. Here, we analyze RctB binding patterns in the V. cholerae genome across various cell cycle stages. We find that RctB primarily binds to sites inhibiting replication initiation at the Chr2 origin (ori2). This inhibitory effect is counteracted when crtS is replicated on Chr1, causing a shift in RctB binding to sites that activate replication at ori2. Structural analyzes indicate the formation of diverse oligomeric states of RctB, coupled to the allosteric effect of DNA, which determine ori2 accessibility. We propose a synchronization model where, upon replication, crtS locally destabilizes the RctB inhibition complex, releasing the Chr2 replication origin., Competing Interests: Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Cell cycle checkpoints are the regulatory mechanisms that secure the strict order of cellular events for cell division that ensure genome integrity. It has been proposed that mitosis initiation depends on the completion of DNA replication, which must be tightly controlled to guarantee genome duplication. Contrary to these conventional hypotheses, we showed here that cells were able to enter mitosis without completion of DNA replication. Although DNA replication was not completed in cells upon depletion of MCM2, CDC45 or GINS4, these under-replicated cells progressed into mitosis, which led to cell death. These unexpected results challenge current model and suggest the absence of a cell cycle checkpoint that monitors the completion of DNA replication., (© The Author(s) 2025. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Cell cycle-dependent gene expression analysis is particularly important as numerous genes show tightly regulated expression patterns at different phases of the cell cycle. For cancer cells, analysis of cell cycle-related events is of paramount significance since tumorigenesis is characteristically coupled to cell cycle perturbations. RT-qPCR is a highly sensitive technique to investigate cell cycle-dependent transcriptional regulation. However, for reliable evaluation of qPCR data reference genes with stable mRNA expression are required. Although several studies investigating cell cycle-dependent gene expression employ frequently used reference genes, the suitability of these reference genes has not been thoroughly investigated so far. Moreover, such potential reference genes for cell cycle analysis have not been described in the literature. Therefore, we aimed to identify reference genes characterized with stable expression throughout the cell cycle in MOLT4 and U937 human leukemia cell lines synchronized with RO-3306 CDK1 inhibitor using RT-qPCR. Here we show that for cell cycle-dependent gene expression analysis the commonly used TBP is suitable, while the recently recognized reference genes SNW1 and CNOT4 are applicable in a cell line-dependent manner. We also suggest that proper selection of reference genes for each experimental condition is crucial for reliable normalization as these aspects can severely compromise conclusions., Competing Interests: Declarations. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Fission yeast is an excellent model system that has been widely used to study the mechanism that control cell cycle progression. However, there is a lack of tools that allow to measure with high precision the duration of the different phases of the cell cycle in individual cells. To circumvent this problem, we have developed a fluorescent reporter that allows the quantification of the different phases of the cell cycle at the single-cell level in most genetic backgrounds. To prove the accuracy of this fluorescent reporter, we have tested the reporter in strains known to have a delay in the G1/S or G2/M transitions, confirming the strength and versatility of the system. An advantage of this reporter is that it eliminates the need for culture synchronization, avoiding stressing the cells. Using this reporter, we show that unperturbed cells lacking Sty1 have a standard cell cycle length and distribution and that the extended length of these cells is due to their increased cell growth rate but not to alterations in their cell cycle progression., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2025 Murciano-Julià et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Human papillomavirus (HPV)-negative head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer type in the world and is associated with an overall poor prognosis. The protein methyltransferase SET and MYND domain-containing 3 (SMYD3), which trimethylates H3K4, activates gene transcription and enhances several oncogenic pathways, including epithelial-mesenchymal transition and cell cycle related pathways, in various cancer types. It was also recently shown that SMYD3 is overexpressed in HPV-negative HNSCC, and represses the expression of type I IFN response genes, contributing to resistance to anti-PD-1 checkpoint blockade in this disease. In this study, we show that SMYD3 depletion using siRNA interference or CRISPR decreases cellular proliferation and clonal capacity, induces cell cycle arrest and decreases the invasive potential of HPV-negative HNSCC cell lines. Accordingly, xenografts of SMYD3 knockout tumors derived from a human HPV-negative HNSCC cell line grew significantly slower compared to control tumors in mice. Genome-wide mapping for SMYD3 and H3K4me3 in HPV-negative HNSCC cells using cleavage under targets and release using nuclease (CUT&RUN) assays identified direct downstream gene targets regulated by SMYD3, including cell cycle- and EMT-promoting genes. This study provides insights into the epigenetic role of SMYD3 as an oncogene in HPV-negative HNSCC and supports SMYD3 as a rational therapeutic target in HPV-negative HNSCC., Competing Interests: Declarations. Competing interests: The authors declare no competing interests., (© 2025. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

Unlike most species that use telomerase for telomere maintenance, many dipterans, including Drosophila , rely on three telomere-specific retrotransposons (TRs)- HeT-A , TART , and TAHRE -to form tandem repeats at chromosome ends. Although TR transcription is crucial in their life cycle, its regulation remains poorly understood. This study identifies the Mediator complex, E2F1-Dp, and Scalloped/dTEAD as key regulators of TR transcription. Reducing the activity of the Mediator or Sd/dTEAD increases TR expression and telomere length, while overexpressing E2F1-Dp or depleting Rbf1 stimulates TR transcription. The Mediator and Sd/dTEAD regulate this process through E2F1-Dp. CUT&RUN (Cleavage under targets and release using nuclease) analysis shows direct binding of CDK8, Dp, and Sd/dTEAD to telomeric repeats, with motif enrichment revealing E2F- and TEAD-binding sites. These findings uncover the Mediator complex's role in controlling TR transcription and telomere length through E2F1-Dp and Sd, coupling the transcriptional regulation of the TR life cycle with host cell-cycle machinery to protect chromosome ends in Drosophila .

Combined removal of Crb1 and Crb2 from the developing optic vesicle evokes cellular and laminar disorganization by disrupting the apical cell-cell adhesion in developing retinal epithelium. As a result, at postnatal stages, affected mouse retinas show temporarily thickened, coarsely laminated retinas in addition to functional deficits, including a severely abnormal electroretinogram and decreased visual acuity. These features are reminiscent of Leber congenital amaurosis 8, which is caused in humans by subsets of Crb1 mutations. However, the cellular basis of the abnormalities in retinal progenitor cells (RPCs) that lead to retinal disorganization is largely unknown. In this study, we analyze specific features of RPCs in mutant retinas, including maintenance of the progenitor pool, cell cycle progression, cell cycle phase-dependent nuclear positioning, cell survival, and generation of mature retinal cell types. We find crucial defects in the mutant RPCs. Upon removal of CRB1 and CRB2, apical structures of the RPCs, determined by markers of cilia and centrosomes, are basally shifted. In addition, the positioning of the somata of the M-phase cells, normally localized at the apical surface of the retinal epithelium, is basally shifted in a nearly randomized pattern along the apico-basal axis. Consequently, we propose that positioning of RPCs is desynchronized from cell cycle phase and largely randomized during embryonic development at E17.5. Because the resultant postmitotic cells inevitably lose positional information, the outer and inner nuclear layers (ONL and INL) fail to form from ONBL during neonatal development and retinal cells become mixed locally and globally. Additional results of the lost tissue polarity in Crb1/Crb2 dKO retinas include atypical formation of heterotopic cell patches containing photoreceptor cells in the ganglion cell layer and acellular patches filled with neural processes. Collectively, these changes lead to a mouse model of LCA8-like pathology. LCA8-like pathology differs substantially from the well-characterized, broad range of degeneration phenotypes that arise during the differentiation of photoreceptor and Muller glial cells in retinitis pigmentosa 12, a closely related disease caused by mutated human Crb1. Importantly, the present results suggest that Crb1/Crb2 serve indispensable functions in maintaining cell-cycle phase-dependent positioning of RPCs along the apico-basal axis, regulating cell cycle progression, and maintaining structural laminar integrity without significantly affecting the size of the RPC pools, generation of the subsets of the retinal cell types, or the distribution of cell cycle phases during RPC division. Taken together, these findings provide the crucial cellular basis of the thickening and severely disorganized lamination that are the unique features of the retinal abnormalities in LCA8 patients., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Ribosome biogenesis (RiBi) is an essential process that controls the protein synthesis rate, but its function in regulating endogenous cardiac regeneration remains unknown. Herein, we investigated the function and underlying mechanism of RiBi-associated circRNAs in cardiomyocyte (CM) proliferation and cardiac regeneration. We used high-throughput sequencing, quantitative PCR and in situ hybridization techniques to identify an adult downregulated circRNA, RiBi-associated circRNA (RBAC), in CMs. A functional study further revealed that RBAC overexpression increased ribosome biogenesis activity and cell cycle progression in CMs, while silencing RBAC decreased ribosome biogenesis activity and cell cycle progression. Moreover, RBAC overexpression induced adult CM proliferation and improved cardiac function after myocardial infarction in adult mice. Mechanistically, RBAC controlled ribosome biogenesis and cell proliferation by regulating the proteasome-dependent degradation of Ddx21, thereby altering the localization of Rps14 and reducing Rb expression. Our findings indicate that RBAC upregulation might be a plausible therapeutic strategy to induce endogenous cardiac regeneration., Competing Interests: Declaration of competing interest The authors have no conflicts of interest to declare., (Copyright © 2024. Published by Elsevier B.V.)

The tumor susceptibility gene 101 (TSG101) was firstly identified as a tumor-inhibiting factor in 1996. Subsequent studies gradually revealed its crucial role in several important cellular processes, including cell survival, vesicle transportation, viral infection, etc. Additionally, TSG101 has been identified as an oncoprotein in certain tumorigenic processes. These conflicting findings suggest that TSG101 might exhibit tumor heterogeneity. Currently, the expression pattern and function of TSG101 in oral squamous cell carcinoma (OSCC) are still untouched. Herein, we reported that TSG101 expression is upregulated and is associated with poorer survival and a higher propensity for lymph node metastasis in OSCC patients. In vivo mouse models confirmed that TSG101 down-regulation effectively inhibited the pulmonary metastases of human OSCC cells. In vitro cell experiments not only proved that TSG101 knockdown significantly disrupted metastasis-related phenotypes in different OSCC cell lines, but also revealed that TSG101 possibly controls the cell cycle through regulating the transcription of Cyclin A/B to play these roles. Additionally, we further validated these findings with a mouse cell line and murine orthotopic OSCC models. Collectively, the oncoprotein function of TSG101 in OSCC is evident from this study. We offer fresh insights into the heterogeneity of TSG101 and highlight new potential targets for OSCC management., Competing Interests: Declaration of competing interest The authors have no relevant financial or non-financial interests to disclose., (Copyright © 2024 Elsevier Inc. All rights reserved.)

The importance of vocal cord leukoplakia (VCL) in the etiology and progression of laryngeal carcinoma has gained increasing recognition. However, research into the mechanisms of laryngeal precancerous lesions such as VCL, has been hampered by the small size of VCL epithelial cells and their limited culture lifespan. In this study, we enhanced the primary culture protocol for VCL epithelial cells and introduced simian virus 40 Large T to establish an immortalized cell line, designated hVCL-MSDEP01. We confirmed that hVCL-MSDEP01 expresses epithelial-specific genes and proteins; it also demonstrates distinct cell cycle dynamics and apoptosis rates compared with primary cells. In conclusion, hVCL-MSDEP01 serves as an ideal in vitro model for studying VCL. This cell line will substantially advance research into the etiology and progression of laryngeal carcinoma., Competing Interests: Competing interests: The authors declare no competing interests. Ethics approval and consent to participate: This study was conducted in accordance with the Declaration of Helsinki and approved by the Ethics Committee of The First Affiliated Hospital, College of Medicine, Zhejiang University, China (Reference Number: IIT20240255B-R1). All participants provided informed consent before participating in the study. Informed Consent Statement: Tissues were collected from discarded samples. And the patient knew and understood the research aims and progress., (© 2024. The Author(s).)

Stimulating cardiomyocyte (CM) dedifferentiation and cell cycle activity (DACCA) is essential for triggering daughter CM formation. In addition to transcriptional processes, RNA-binding proteins (RBPs) are emerging as crucial post-transcriptional players in regulating CM DACCA. However, whether post-transcriptional regulation of CM DACCA by RBPs could effectively trigger daughter CM formation remains unknown. By performing integrated bioinformatic analysis of snRNA-seq data from neonatal and adult hearts, this study identified Hnrnpa1 as a potential RBP regulating CM DACCA. Hnrnpa1 expression decreased significantly during postnatal heart development. With the use of α-MHC-H2B-mCh/CAG-eGFP-anillin transgenic mice, Hnrnpa1 overexpression promoted CM DACCA, thereby triggering daughter CM formation and enhancing cardiac repair after myocardial infarction (MI). In contrast, CRISPR/Cas9 technology is used to generate CM-specific Hnrnpa1 knockout mice. Hnrnpa1 knockout inhibited cardiac regeneration and worsened cardiac function in the neonatal MI model. Nanopore RNA sequencing, RIP assay, IP-MS, MeRIP-qPCR, PAR-CLIP and luciferase reporter experiments showed that Hnrnpa1 induced Mettl3 post-transcriptional splicing to inhibit m6A-dependent Pbx1 and E2F1 degradation, thereby increasing Runx1, Ccne1, Cdk2 and Ccnb2 expression to promote CM DACCA. In conclusion, Hnrnpa1 triggered daughter CM formation by promoting CM DACCA in a post-transcriptional manner, indicating that Hnrnpa1 might serve as a promising target in cardiac repair post-MI., (© 2024 The Author(s). Advanced Science published by Wiley‐VCH GmbH.)

DNA damage repair (DDR) proteins are well recognized as guardians of the genome that are frequently lost during malignant transformation of normal cells across cancer types. To date, their tumor suppressor functions have been generally regarded as a consequence of their roles in maintaining genomic stability: more genomic instability increases the risk of oncogenic transformation events. However, recent discoveries centering around DNA mismatch repair (MMR) proteins suggest a broader impact of the loss of DDR proteins on cellular processes beyond genomic instability. Here, we explore the clinical implications of nonrepair roles for DDR proteins, using the growing evidence supporting roles for DNA MMR proteins in cell cycle and apoptosis regulation, metabolic function, the cellular secretome, and immunomodulation., Competing Interests: Declaration of interests S.H. serves as a member of the California Breast Cancer Research Program and has two provisional patent applications relating to a role for DNA repair proteins in cell cycle regulation (Serial Nos: 62/670,368, 63/106777). The remaining authors have no interests to declare., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Estrogen‑related receptor (ERR) is an orphan nuclear receptor structurally akin to the estrogen receptor. ERR is expressed in tissues with active energy metabolism and regulates intracellular metabolic functions. Additionally, ERRs are known to be strongly expressed in the epidermis of skin tissue, but their functions are unknown. The present study investigated the function of ERRα in human skin fibroblasts. ERRα expressed in human dermal fibroblast TIG113 was knocked down using small interfering (si)RNA and gene expression was comprehensively analyzed using microarrays 48 h later. Pathway analysis was performed using Wikipathways on genes exhibiting expression changes of ≥1.5‑fold. Expression of cell cycle‑related and apoptosis‑related genes was compared using reverse transcription‑quantitative PCR. After treating TIG113 cells with siERRα for 72 h, cell proliferation was assessed using the Cell Counting Kit‑8 or a scratch wound healing assay and apoptotic cells were measured using the Poly Caspase Assay Kit. Cell cycle analysis was performed using flow cytometry. The expression of the ERRα gene was suppressed by siRNA. The expression of genes associated with cell cycle‑related pathways were decreased while that of those associated with apoptosis‑related pathways increased. Furthermore, the expression of cell cycle‑related genes such as cell division cycle 25C, cyclin E and cyclin B1 was decreased and the expression of apoptosis‑related genes such as caspase3 and Fas cell surface death receptor was increased. Cell proliferation was suppressed and the number of apoptotic cells increased ~2‑fold in ERRα‑knockdown TIG113 cells. Cell cycle analysis revealed that the number of cells in the Sub‑G 1 phase increased and that in the S and G 2 /M phases decreased. The present study suggested that ERRα is an essential for the survival of human skin fibroblasts.

Improved understanding of cardiomyocyte (CM) cell cycle regulation may allow researchers to stimulate pro-regenerative effects in injured hearts or promote maturation of human stem cell-derived CMs. Gene therapies, in particular, hold promise to induce controlled proliferation of endogenous or transplanted CMs via transient activation of mitogenic processes. Methods to identify and characterize candidate cardiac mitogens in vitro can accelerate translational efforts and contribute to the understanding of the complex regulatory landscape of CM proliferation and postnatal maturation. In this study, A CRISPR knockout-based screening strategy using in vitro neonatal rat ventricular myocyte (NRVM) monolayers is established, followed by candidate mitogen validation in mature 3-D engineered cardiac tissues (ECTs). This screen identified knockout of the purine metabolism enzyme adenosine deaminase (ADA-KO) as an effective pro-mitogenic stimulus. RNA-sequencing of ECTs further reveals increased pentose phosphate pathway (PPP) activity as the primary driver of ADA-KO-induced CM cycling. Inhibition of the pathway's rate limiting enzyme, glucose-6-phosphate dehydrogenase (G6PD), prevented ADA-KO induced CM cycling, while increasing PPP activity via G6PD overexpression increased CM cycling. Together, this study demonstrates the development and application of a genetic/tissue engineering platform for in vitro discovery and validation of new candidate mitogens affecting regenerative or maturation states of cardiomyocytes., (© 2024 Wiley‐VCH GmbH.)

The recurrence of glioma after treatment has remained an intractable problem for many years. Recently, numerous studies have explored the pivotal role of the mouse double minute 2 (MDM2)/p53 pathway in cancer treatment. Lysine phosphate phosphohistidine inorganic pyrophosphate phosphatase (LHPP), a newly discovered tumor suppressor, has been confirmed in numerous studies on tumors, but its role in glioma remains poorly understood. Expression matrices in The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) databases were analyzed using gene set enrichment analysis (GSEA), revealing significant alterations in the p53 pathway among glioma patients with high LHPP expression. The overexpression of LHPP in glioma cells resulted in a reduction in cell proliferation, migration, and invasive ability, as well as an increase in apoptosis and alterations to the cell cycle. The present study has identified a novel inhibitory mechanism of LHPP against glioma, both in vivo and in vitro. The results demonstrate that LHPP exerts anti-glioma effects via the MDM2/p53 pathway. These findings may offer a new perspective for the treatment of glioma in the clinic., Competing Interests: Declaration of competing interest The authors declare no potential competing interests., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Cellular senescence prevents the application of mesenchymal stem cells in tissue engineering and stem cell therapy. Effective regulation of senescence is the key to maintain the functional stability of mesenchymal stem cells and improve their clinical application. This study aims to explore the molecular mechanism changes in human dental pulp stem cells (hDPSCs) during replicative senescence, focusing on the potential role of pregnancy-specific glycoprotein (PSGs) family member PSG4 in modulating cellular senescence. RNA sequencing was performed on hDPSCs at different passages and with PSG4 overexpression to reveal changes in gene expression during the process. Gain- and loss-of-function studies suggested that PSG4 regulated cellular senescence. PSG4 expression levels were significantly elevated during cellular senescence and closely correlated with cell cycle regulation. This study provides new insights into the molecular mechanisms underlying of hDPSCs' replicative senescence. PSG4 acts as a pivotal regulator of replicative senescence in hDPSCs by impacting cell cycle process., Competing Interests: Declaration of Competing Interest The authors state that they have no conflicts of interest to this study., (Copyright © 2025 Elsevier Ltd. All rights reserved.)

The primary objective of this study was to conduct a comprehensive analysis of the mechanism by which TCF7 recombinant protein operates, as well as to examine its expression patterns within bladder cancer cells. This research seeks to establish a new theoretical framework and provide experimental data that could advance the field of molecular targeted therapy for bladder cancer. Erlotinib, a well-known targeted therapy drug, was administered to the bladder cancer cells, and we evaluated its antitumor effects through various assays such as cell proliferation, apoptosis, and cell cycle analysis. To delve deeper into the mechanisms of action associated with the TCF7 recombinant protein, we conducted extensive analyses of signaling pathways as well as gene expression profiles. The findings indicated a significant correlation between the expression levels of TCF7 in bladder cancer cells and the tumor's malignancy grade. Following the treatment with Erlotinib, we observed a marked inhibition of cell proliferation, an increase in apoptotic activity, and notable alterations in cell cycle distribution. The results suggested that the molecules of the TCF7 recombinant protein could potentially influence the biological characteristics and behavior of bladder cancer cells by modulating specific signaling pathways, particularly the Wnt/β-catenin signaling pathway. Further analysis of the gene expression profiles also enabled us to identify downstream target genes associated with TCF7, ultimately shedding light on its specific mechanisms of action in the context of bladder cancer., Competing Interests: Declaration of competing interest The authors declare no competing interests., (Copyright © 2025 Elsevier B.V. All rights reserved.)

Current cancer burden caused by persistent infection with human papillomaviruse genotype 16 (HPV16) cannot be ignored. The related mechanisms of oncoproteins E6 and E7 from HPV16 on keratinocyte malignant transformation need to be further elucidated. GSE3292 dataset analysis revealed the upregulation of ETS transcription factor 3 (ELF3) and cyclin E2 (CCNE2). To verify whether there is an interaction between ELF3 and CCNE2, E74 like ELF3 and CCNE2 expression profiles as well as their putative binding sites were analyzed using bioinformatics. Retroviruses encoding HPV16 E6 and E7 genes were used to induce immortalization of human foreskin keratinocytes (HFKs) in vitro. Dual luciferase reporters assay was used to verify the binding of ELF3 and CCNE2. The effect of ELF3 on the immortalized cells was investigated using CCK-8 assay, cell cycle analysis and western blot. ELF3 and CCNE2 presented overexpression patterns in head and neck squamous cell carcinoma. HPV16 E6/E7-expressing HFKs showed enhanced viability, accelerated cell cycle as well as upregulated ELF3 and CCNE2. ELF3 overexpression enhanced the activity of CCNE2 promoter. ELF3 silencing reduced viability, induced cell cycle arrest and suppressed expressions of CCNE2, E6 and E7 in HPV16 E6/E7-expressing HFKs. Downregulation of ELF3 played an inhibiting role in the malignant transformation of HPV16 E6/E7-immortalized HFKs by decreasing CCNE2 expression.

Mammalian genomes host a diverse array of RNA that includes protein-coding and noncoding transcripts. However, the functional roles of most long noncoding RNAs (lncRNAs) remain elusive. Using RNA-targeting CRISPR-Cas13 screens, we probed how the loss of ∼6,200 lncRNAs impacts cell fitness across five human cell lines and identified 778 lncRNAs with context-specific or broad essentiality. We confirm their essentiality with individual perturbations and find that the majority of essential lncRNAs operate independently of their nearest protein-coding genes. Using transcriptome profiling in single cells, we discover that the loss of essential lncRNAs impairs cell-cycle progression and drives apoptosis. Many essential lncRNAs demonstrate dynamic expression across tissues during development. Using ∼9,000 primary tumors, we pinpoint those lncRNAs whose expression in tumors correlates with survival, yielding new biomarkers and potential therapeutic targets. This transcriptome-wide survey of functional lncRNAs advances our understanding of noncoding transcripts and demonstrates the potential of transcriptome-scale noncoding screens with Cas13., Competing Interests: Declaration of interests The New York Genome Center and New York University have applied for patents related to the work in this article. H.-H.W. is a cofounder of Neptune Bio. N.E.S. is an advisor to Qiagen and a cofounder and advisor of OverT Bio and TruEdit Bio., (Copyright © 2024 Elsevier Inc. All rights reserved.)

A poorer prognosis is thought to be associated with "double expressor lymphomas," which are a subtype of diffuse large B cell lymphomas (DLBCL) that co-express MYC and BCL2. While the role of ubiquitin-specific peptidase 37 (USP37) in lung cancer, where it mediates the deubiquitination and stabilization of c-myc, has been well-documented, its involvement in DLBCL remains unexplored. The use of RT-PCR, immunohistochemistry, or WB test allowed for the detection of elevated USP37 in DLBCL tissues and cells. In order to understand the function of USP37 in DLBCL, keloid DLBCL cells were transfected with si-USP37 using Lipofectamine 3000. When tested on DLBCL cells, USP37 increased cell proliferation and inhibited cell cycle progression. USP37 controls the process of deubiquitination to stabilise c-myc proteins. The overexpression of c-Myc facilitated cell proliferation and prevented the cell cycle of DLBCL cells stimulated by si-USP37, which should be taken into consideration. Furthermore, USP37 depletion consistently hinders the development of tumour xenografts in mouse models. Overexpressing c-myc, however, may partially counteract this impact. The data show that USP37 may be a potential therapeutic target for DLBCL, and that it may enhance the course of the disease by deubiquitinating c-myc via direct interactions with c-myc., Competing Interests: Declarations. Competing interests: The authors declare no competing interests. Ethical approval: Experiments had been approved by the Research Ethics Committee of the The Affiliated Hospital of Qingdao University (QYFY-WZLL-28458). Consent to participate: Not applicable. Consent for publication: Not applicable., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

Human papillomavirus (HPV) is a prevalent sexually transmitted infection, implicated in various cancers, yet its influence in non-cancerous oesophageal tissue remains unclear. This study aims to investigate the gene expression changes associated with high-risk HPV (HR-HPV) in non-cancerous oesophageal tissue to elucidate potential early oncogenic mechanisms. Using RNA sequencing, we compared transcriptomic profiles of HPV-positive and HPV-negative non-cancerous oesophageal tissues. Differential gene expression analysis revealed significant upregulation of cell cycle and DNA replication pathways in HPV-positive samples, specifically involving key genes such as CCNA2 , DSN1 , and MCM10 , which are known to regulate cellular proliferation and genomic stability. Additionally, kinase and transcription factor enrichment analyses highlighted HR-HPV-associated regulatory molecules, including E2F4 and CSNK2A1, suggesting HPV's role in modulating host cell cycle control. These findings support the hypothesis that HPV infection may initiate cellular alterations in oesophageal tissue, potentially predisposing it to malignancy. This study contributes to understanding HPV's impact in non-cancerous tissues and identifies possible biomarkers for early HPV-related cellular changes, offering insights into HPV-driven cancer development beyond traditionally associated sites.

Elevated stress signaling compromises plant growth by suppressing proliferative and formative division in the meristem. Plant elicitor peptide, an endogenous danger signal triggered by biotic and abiotic stresses in Arabidopsis (Arabidopsis thaliana), suppresses proliferative division, alters xylem vessel organization, and disrupts cell-to-cell symplastic connections in roots. To gain insight into the dynamic molecular framework that modulates root development under elevated danger signals, we performed a time-course RNA-sequencing analysis of the root meristem after synthetic PEP1 treatment. Our analyses revealed that SALT TOLERANCE ZINC FINGER (STZ) and its homologs are a potential nexus between the stress response and proliferative cell cycle regulation. Through functional, phenotypic, and transcriptomic analyses, we observed that STZ differentially controls the cell cycle, cell differentiation, and stress response genes in various tissue layers of the root meristem. Moreover, we determined the STZ expression level critical for enabling the growth-defense tradeoff. These findings provide valuable information about the dynamic gene expression changes that occur upon perceiving danger signals in the root meristem and potential engineering strategies to generate stress-resilient plants., Competing Interests: Conflict of interest statement. None declared., (© The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists.)

Background: The fatal diffuse midline gliomas (DMG) are characterized by an undruggable H3K27M mutation in H3.1 or H3.3. K27M impairs normal development by stalling differentiation. The identification of targetable pathways remains very poorly explored. Toward this goal, we undertake a multi-omics approach to evaluate replication timing profiles, transcriptomics, and cell cycle features in DMG cells from both H3.1K27M and H3.3K27M subgroups and perform a comparative, integrative data analysis with healthy brain tissue., Results: DMG cells present differential replication timing in each subgroup, which, in turn, correlates with significant differential gene expression. Differentially expressed genes in S phase are involved in various pathways related to DNA replication. We detect increased expression of DNA replication genes earlier in the cell cycle in DMG cell lines compared to normal brain cells. Furthermore, the distance between origins of replication in DMG cells is smaller than in normal brain cells and their fork speed is slower, a read-out of replication stress. Consistent with these findings, DMG tumors present high replication stress signatures in comparison to normal brain cells. Finally, DMG cells are specifically sensitive to replication stress therapy., Conclusions: This whole genome multi-omics approach provides insights into the cell cycle regulation of DMG via the H3K27M mutations and establishes a pharmacologic vulnerability in DNA replication, which resolves a potentially novel therapeutic strategy for this non-curable disease., Competing Interests: Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: MGF is a consultant for Blueprint Medicines; other authors declare no conflicts of interest., (© 2024. The Author(s).)

Zeste white 10 (ZW10) was first identified as a centromere/kinetochore protein encoded by the ZW10 gene in Drosophila. ZW10 guides the spindle assembly checkpoint signaling during mitotic chromosome segregation in metazoans. Recent studies have shown that ZW10 is also involved in membrane-bound organelle interactions during interphase and plays a vital role in membrane transport between the endoplasmic reticulum and Golgi apparatus. Despite these findings, the precise molecular mechanisms by which ZW10 regulates interactions between membrane-bound organelles in interphase and the assembly of membraneless organelle kinetochore in mitosis remain elusive. Here, we highlight how ZW10 forms context-dependent protein complexes during the cell cycle. These complexes are essential for mediating membrane trafficking in interphase and ensuring the accurate segregation of chromosomes in mitosis., (© The Author(s) (2024). Published by Oxford University Press on behalf of Journal of Molecular Cell Biology, CEMCS, CAS.)